# Usegalaxy, ChIPSeq, bedtools Intersect intervals, Blacklist regions

**URL:** <https://help.galaxyproject.org/t/usegalaxy-chipseq-bedtools-intersect-intervals-blacklist-regions/4296>\
**Category:** usegalaxy.org support\
**Tags:** epigenetics\
**Created:** [August 14, 2020, 2:27pm UTC](https://help.galaxyproject.org/t/usegalaxy-chipseq-bedtools-intersect-intervals-blacklist-regions/4296 "2020-08-14T14:27:42Z")\
**Posts on this page:** 1\
**Showing post:** 1

<div class="post-metadata">

**Author:** ![shamjdeed](https://avatars.discourse-cdn.com/v4/letter/s/df788c/32.png) [@shamjdeed](https://help.galaxyproject.org/u/shamjdeed)\
**Post date:** [August 14, 2020, 2:27pm UTC](https://help.galaxyproject.org/t/usegalaxy-chipseq-bedtools-intersect-intervals-blacklist-regions/4296/1 "2020-08-14T14:27:42Z")

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Hello,  
I am trying to remove the blacklisted regions from my ChIP-Seq datasets (Mapped regions to hg19 human genome, BAM files) using **bedtools Intersect intervals** (Galaxy Version 2.29.2), I used to do that for my previous datasets and it worked well, However, yesterday and today I am trying the same steps and I am getting this message:

The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool with id ‘toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools\_intersectbed/2.29.2’: The effective dataset identifier consumed by object store [id] must be set before a path can be constructed.

{  
“history\_id”: “5afb961e3bb083e1”,  
“tool\_id”: “toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools\_intersectbed/2.29.2”,  
“tool\_version”: “2.29.2”,  
“inputs”: {  
“inputA”: {  
“values”: [  
{  
“id”: “11ac94870d0bb33af8237d1cea946e20”,  
“hid”: 32,  
“name”: “Veh-ARID1A-hTret-SJ77-Part2.Bowtie2 on data 19: alignments”,  
“tags”: [],  
“src”: “hda”,  
“keep”: false  
}  
],  
“batch”: false  
},  
“reduce\_or\_iterate|reduce\_or\_iterate\_selector”: “iterate”,  
“reduce\_or\_iterate|inputB”: {  
“values”: [  
{  
“id”: “11ac94870d0bb33ab8996efdd404730b”,  
“hid”: 31,  
“name”: “Galaxy39-[Galaxy114-[hg19-blacklist.v2.bed.gz].bed].bed”,  
“tags”: [],  
“src”: “hda”,  
“keep”: false  
}  
],  
“batch”: false  
},  
“strand”: “”,  
“overlap\_mode”: null,  
“split”: “false”,  
“fraction\_cond|fraction\_select”: “default”,  
“invert”: “true”,  
“once”: “false”,  
“count”: “false”,  
“bed”: “false”,  
“sorted”: “false”,  
“header”: “false”  
}  
}

Could you please help,  
Thank you very much!  
Sham

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_[View the full topic](https://help.galaxyproject.org/t/usegalaxy-chipseq-bedtools-intersect-intervals-blacklist-regions/4296)._